Microarray preparation methods for synthetic oligomers, including oligonucleotides (oligos) include the following: (i) spotting a solution on a prepared flat or substantially planar surface using spotting robots; (ii) in situ synthesis by printing reagents via ink jet or other computer printing technology and using standard phosphoramidite chemistry; (iii) in situ parallel synthesis using electrochemically generated acid for removal of protecting groups and using standard phosphoramidite chemistry; (iv) in situ synthesis using maskless photo-generated acid for removal of protecting groups and using regular phosphoramidite chemistry; (v) mask-directed in situ parallel synthesis using photo-cleavage of photolabile protecting groups (PLPG) and standard phosphoramidite chemistry; (vi) maskless in situ parallel synthesis using PLPG and digital photolithography and standard phosphoramidite chemistry; and (vii) electric field attraction/repulsion for depositing fully formed oligos onto known locations.
Photolithographic techniques for in situ oligo synthesis are disclosed in Fodor et al. U.S. Pat. No. 5,445,934 and the additional patents claiming priority thereto, all of which are incorporated by reference herein. Electric field attraction/repulsion microarrays are disclosed in Hollis et al. U.S. Pat. No. 5,653,939 and Heller et al. U.S. Pat. No. 5,929,208, both of which are incorporated by reference herein. An electrode microarray for in situ oligo synthesis using electrochemical deblocking is disclosed in Montgomery U.S. Pat. Nos. 6,093,302; 6,280,595, and 6,444,111 (Montgomery I, II, and III respectively), all of which are incorporated by reference herein. Another and materially different electrode array (not a microarray) for in situ oligo synthesis on surfaces separate and apart from electrodes using electrochemical deblocking is disclosed in Southern U.S. Pat. No. 5,667,667, which is incorporated by reference herein. A review of oligo microarray synthesis is provided by: Gao et al., Biopolymers 2004, 73:579.
U.S. patent application Ser. No. 10/243,367, filed 12 Sep. 2002 (Oleinikov) discloses a process for assembling a polynucleotide from a plurality of oligonucleotides. The claimed process provides a plurality of oligonucleotide sequences that are synthesized in situ or spotted on a microarray device. The plurality of oligonucleotide sequences is attached to a solid or porous surface of the microarray device. The oligonucleotide sequences are cleaved at a cleavable linker site to form a soluble mixture of oligonucleotides. The cleavable linker is a chemical composition having a succinate moiety bound to a nucleotide moiety such that cleavage produces a 3′-hydroxy nucleotide.
The succinate moiety disclosed in Oleinikov as a cleavable linker is bound to the solid or porous surface through an ester linkage by reacting the succinate moieties with the solid or porous surface. In general, formation of an ester linkage to an organic hydroxyl on a solid surface using a succinate is relatively difficult and often results in relatively low yield. Additionally, the reaction conditions require a relatively long period of time at relatively high temperature. Increasing yield would increase oligonucleotide density and provide more efficient production of oligonucleotides on a microarray. Oligonucleotides cleaved from the microarray disclosed in Oleinikov have a three prime hydroxyl, which may limit the use of such oligonucleotides or result in the need for an additional step to modify the three-prime hydroxyl. Disclosed herein are embodiments that provide oligonucleotides having three-prime functionality that is different from a three prime hydroxyl of Oleinikov, of which different functionality expands the use of such oligonucleotides. Further disclosed herein are embodiments that address the problems in Oleinikov of low yield and hence low oligonucleotide density at a location on a microarray by providing alternative cleavable linker chemistry, which is more reactive to hydroxyl groups on a microarray. Further disclosed herein are embodiments that address the limitations of Oleinikov with respect to attachment of oligonucleotides having a three-prime hydroxyl to a solid or porous surface by providing different three-prime chemistry.